Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021870.1 Corchorus olitorius cultivar O-4 contig21903, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19313
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Found at i:827 original size:19 final size:19
Alignment explanation
Indices: 805--845 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
795 CTTTTATTTC
805 TTTTATT-TTCTTTTTCCCT
1 TTTTATTATTCTTTTT-CCT
*
824 TTTTTTTATTCTTTTTCCT
1 TTTTATTATTCTTTTTCCT
843 TTT
1 TTT
846 CTTTTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTATTCTTTTTCCT
Found at i:828 original size:20 final size:19
Alignment explanation
Indices: 812--850 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
802 TTCTTTTATT
812 TTCTTTTTCCCTTTTTTTTA
1 TTCTTTTT-CCTTTTTTTTA
832 TTCTTTTTCCTTTTCTTTT
1 TTCTTTTTCCTTTT-TTTT
851 CCTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTTCCTTTTTTTTA
Found at i:838 original size:30 final size:30
Alignment explanation
Indices: 791--864 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
781 ATTCTAAAAT
791 TTTTCTTTTATT-TCTTTT-ATTTTCTTTTTCCC
1 TTTT-TTTTATTCT-TTTTCATTTTC-TTTT-CC
*
823 TTTTTTTTATTCTTTTTCCTTTTCTTTTCC
1 TTTTTTTTATTCTTTTTCATTTTCTTTTCC
*
853 TTTTCTTTATTC
1 TTTTTTTTATTC
865 CAAAATGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 13 0.34
31 15 0.39
32 10 0.26
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTTTTATTCTTTTTCATTTTCTTTTCC
Found at i:850 original size:11 final size:11
Alignment explanation
Indices: 836--860 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
826 TTTTTATTCT
836 TTTTCCTTTTC
1 TTTTCCTTTTC
847 TTTTCCTTTTC
1 TTTTCCTTTTC
858 TTT
1 TTT
861 ATTCCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCCTTTTC
Found at i:992 original size:37 final size:37
Alignment explanation
Indices: 940--1020 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
930 GGCCCAAGCT
*
940 TGGGCCAAGCTCTGGCCCACGCGCCAGGCCTAGCGCC
1 TGGGCCAAGCGCTGGCCCACGCGCCAGGCCTAGCGCC
* * *
977 TGGGCCAAGCGCTGGCCCACGCGTCTGGCCTGGCGCC
1 TGGGCCAAGCGCTGGCCCACGCGCCAGGCCTAGCGCC
1014 TGGGCCA
1 TGGGCCA
1021 GCAAGGCCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.11, C:0.41, G:0.36, T:0.12
Consensus pattern (37 bp):
TGGGCCAAGCGCTGGCCCACGCGCCAGGCCTAGCGCC
Found at i:4822 original size:48 final size:48
Alignment explanation
Indices: 4751--4974 Score: 249
Period size: 48 Copynumber: 4.8 Consensus size: 48
4741 TTAGGATGCC
4751 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
1 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
* * * *
4799 TTATGCCATCACTGCCTTTCTCTTGAGGCTCATACATATTAGAATCA-
1 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
* * * * * *
4846 TTATGCCATCACTGCCATACTTTTCAGTCTCATCCATATCAGAACCAT
1 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
* * * *
4894 CTATGCCATCAGTGCCTTGCTCTTGAGCTTCATCCATATC---ACCAT
1 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
* * * * *
4939 TTATACCATCATTGCCTTGTTCTTGAGTCTCTTCCA
1 TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCA
4975 CGAGAAAACC
Statistics
Matches: 148, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
45 34 0.23
47 39 0.26
48 75 0.51
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.36
Consensus pattern (48 bp):
TTATGCCATCACTGCCTTGCTCTTGAGCCTCATCCATATCAGAATCAT
Found at i:9039 original size:346 final size:344
Alignment explanation
Indices: 8406--9096 Score: 1265
Period size: 346 Copynumber: 2.0 Consensus size: 344
8396 AATTATACAC
* **
8406 ATAAACAAACAAAAATAGTTGAAGTGTGAATTACATCAAGGTTAACCTTATTCTCTCACCACATT
1 ATAAACAAACAAAAATAGTTGAAGTGTGAATTACACCAAGGGCAACCTTATTCTCTCACCACATT
8471 CATTTGGGTACTATTTGCATGGTTTTTGTGTCTTTTTGCGTAAGGTTTTTTTGTTATTTCGTAGA
66 CATTTGGGTACTATTTGCATGGTTTTTGTGTCTTTTTGCGTAAGGTTTTTTTGTTATTTCGTAGA
8536 ACTCTTAGGGGTAGTCCGGGCATTCCGATCCTGTTTTGCCCTCCAACATTGGTTTTCATGTAATT
131 ACTCTTAGGGGTAGTCCGGGCATTCCGATCCTGTTTTGCCCTCCAACATTGGTTTTCATGTAATT
8601 TGGTGTAGTTGGCAAGAGTGAACATGGTTGTTCATGGTTTTTCTTTTTATCTCACCTAGGGTTTA
196 TGGTGTAGTTGGCAAGAGTGAACATGGTTGTTCATGGTTTTTCTTTTTATCTCACCTAGGGTTTA
8666 TGTTGTATGTTAGGGTTTGGCTTTCATGTCATGGGAGACAATGTTTCATCTCACTTAGGGTTTGT
261 TGTTGTATGTTAGGGTTTGGCTTTCATGTCATGGGAGACAATGTTTCATCTCACTTAGGGTTTGT
*
8731 CATGTCATGGTTAGGGTTT
326 CATGTCATGGCTAGGGTTT
*
8750 ATAAACAAACAATAATAGTTGAAGTGTGAATTACACCAAGGGCAACCTTATTCTCTCACCACATT
1 ATAAACAAACAAAAATAGTTGAAGTGTGAATTACACCAAGGGCAACCTTATTCTCTCACCACATT
*
8815 CATTTGGGATACTATTTGCATGGTTTTTGTGTCTTTTTGCGTATGGTTTTTTTGTTATTTCGTAG
66 CATTTGGG-TACTATTTGCATGGTTTTTGTGTCTTTTTGCGTAAGGTTTTTTTGTTATTTCGTAG
* * *
8880 AACTCTTAGGGGTAGTCCGGGCATTCCGATCCTTTTTTGCTCTCCACCATTTGGTTTTCATGTAA
130 AACTCTTAGGGGTAGTCCGGGCATTCCGATCCTGTTTTGCCCTCCAACA-TTGGTTTTCATGTAA
*
8945 TTTGGTGTAGTTGGCAAGGGTGAACATGGTTGTTCATGGTTTTTCTTTTTATCTCACCTAGGGTT
194 TTTGGTGTAGTTGGCAAGAGTGAACATGGTTGTTCATGGTTTTTCTTTTTATCTCACCTAGGGTT
*
9010 TATGTTGTATGTTAGGGTTTGGGTTTCATGTCATGGGAGACAATGTTTCATCTCACTTAGGGTTT
259 TATGTTGTATGTTAGGGTTTGGCTTTCATGTCATGGGAGACAATGTTTCATCTCACTTAGGGTTT
9075 GTCATGTCATGGCTAGGGTTT
324 GTCATGTCATGGCTAGGGTTT
9096 A
1 A
9097 GATTTCATGT
Statistics
Matches: 334, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
344 69 0.21
345 101 0.30
346 164 0.49
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (344 bp):
ATAAACAAACAAAAATAGTTGAAGTGTGAATTACACCAAGGGCAACCTTATTCTCTCACCACATT
CATTTGGGTACTATTTGCATGGTTTTTGTGTCTTTTTGCGTAAGGTTTTTTTGTTATTTCGTAGA
ACTCTTAGGGGTAGTCCGGGCATTCCGATCCTGTTTTGCCCTCCAACATTGGTTTTCATGTAATT
TGGTGTAGTTGGCAAGAGTGAACATGGTTGTTCATGGTTTTTCTTTTTATCTCACCTAGGGTTTA
TGTTGTATGTTAGGGTTTGGCTTTCATGTCATGGGAGACAATGTTTCATCTCACTTAGGGTTTGT
CATGTCATGGCTAGGGTTT
Found at i:11526 original size:24 final size:25
Alignment explanation
Indices: 11473--11529 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
11463 AGTCTTTTGC
* *
11473 TCATTTTCTATGTATATCTATAATG
1 TCATTTTCTATATATATCCATAATG
*
11498 CCATTTTCT-TATATATTCCAT-ATG
1 TCATTTTCTATATATA-TCCATAATG
11522 TCATTTTC
1 TCATTTTC
11530 AGTTATGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.53
Consensus pattern (25 bp):
TCATTTTCTATATATATCCATAATG
Found at i:13770 original size:12 final size:12
Alignment explanation
Indices: 13748--13778 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13738 TTTTAACTTT
13748 CACGT-ACGTTG
1 CACGTGACGTTG
13759 CACGTGACGTTG
1 CACGTGACGTTG
13771 CACGTGAC
1 CACGTGAC
13779 CTAACGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (12 bp):
CACGTGACGTTG
Found at i:13964 original size:22 final size:20
Alignment explanation
Indices: 13928--13972 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
13918 ATTTGAGAAC
*
13928 CCTTTTATAAATTTTTTTAA
1 CCTTTTATAAATTTTGTTAA
13948 CCTTCTTATGAAATTTTGTTAA
1 CCTT-TTAT-AAATTTTGTTAA
13970 CCT
1 CCT
13973 CCCTAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (20 bp):
CCTTTTATAAATTTTGTTAA
Found at i:14055 original size:22 final size:23
Alignment explanation
Indices: 13998--14061 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
13988 AAGACCTCAT
*
13998 TATGAAATTTTGATAACCAACAC
1 TATGAAATATTGATAACCAACAC
* * **
14021 TATGAGATGTTGATAACCTCCA-
1 TATGAAATATTGATAACCAACAC
*
14043 TATGATATATTGATAACCA
1 TATGAAATATTGATAACCA
14062 CGTTATGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (23 bp):
TATGAAATATTGATAACCAACAC
Found at i:14068 original size:22 final size:22
Alignment explanation
Indices: 13995--14073 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
13985 TTGAAGACCT
*
13995 CATTATGAAATTTTGATAACCAA
1 CATTATGAAATATTGATAACC-A
* * * *
14018 CACTATGAGATGTTGATAACCTC
1 CATTATGAAATATTGATAACC-A
*
14041 CA-TATGATATATTGATAACCA
1 CATTATGAAATATTGATAACCA
*
14062 CGTTATGGAAAT
1 CATTAT-GAAAT
14074 TTAAAAACCT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.02
22 19 0.43
23 24 0.55
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (22 bp):
CATTATGAAATATTGATAACCA
Found at i:14129 original size:22 final size:22
Alignment explanation
Indices: 14106--14379 Score: 198
Period size: 22 Copynumber: 12.8 Consensus size: 22
14096 TTAGTATTCA
* *
14106 CACTCTGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
*
14128 CACTATGAAATTGTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * * *
14150 CGCTATAAAATTTTAATAAACCA
1 CACTATGAAATTTTGAT-AACCT
* * *
14173 CCCTATAAAATTTTAATAACCT
1 CACTATGAAATTTTGATAACCT
*
14195 C-CTTATGAAATCTTGATAA-CT
1 CAC-TATGAAATTTTGATAACCT
14216 -AC-A--AAA-TTTGATAACCT
1 CACTATGAAATTTTGATAACCT
**
14233 C-CATATGATTTTTTGATAACCT
1 CAC-TATGAAATTTTGATAACCT
* *
14255 CA-TCATGAAATTTTGTTAATCT
1 CACT-ATGAAATTTTGATAACCT
*
14277 CCCTATGAAATTTTGATAACCCT
1 CACTATGAAATTTTGATAA-CCT
* *
14300 C-TTATGAAATTTTGA-AAACT
1 CACTATGAAATTTTGATAACCT
*
14320 AAACTATGAAATTTTGATAACCTT
1 -CACTATGAAATTTTGATAACC-T
*
14344 CA-TATGAAATTTTGATATCCT
1 CACTATGAAATTTTGATAACCT
*
14365 C-C-CTGAAATTTTGAT
1 CACTATGAAATTTTGAT
14380 TACTCCATAG
Statistics
Matches: 202, Mismatches: 31, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
16 7 0.03
17 6 0.03
19 2 0.01
20 14 0.07
21 10 0.05
22 134 0.66
23 28 0.14
24 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.37
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:14161 original size:44 final size:42
Alignment explanation
Indices: 14111--15132 Score: 340
Period size: 44 Copynumber: 23.9 Consensus size: 42
14101 ATTCACACTC
*
14111 TGAAATTTTGATAACCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCTC-CTA
* * * * *
14155 TAAAATTTTAATAAACCACCCTATAAAATTTTAATAACCTCCTTA
1 TGAAATTTTGAT-AACC-CACTATGAAATTTTGATAACCTCC-TA
* *
14200 TGAAATCTTGATAA-CTAC-A--AAA-TTTGATAACCTCCATA
1 TGAAATTTTGATAACCCACTATGAAATTTTGATAACCTCC-TA
** * *
14238 TGATTTTTTGATAACCTCA-TCATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACC-CACT-ATGAAATTTTGATAACCT-CCTA
* * *
14282 TGAAATTTTGATAACCCTCTTATGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCCAC-TATGAAATTTTGATAACCT--CCTA
* *
14326 TGAAATTTTGATAACCTTCA-TATGAAATTTTGATATCCTCC-C
1 TGAAATTTTGATAACC--CACTATGAAATTTTGATAACCTCCTA
* * * *
14368 TGAAATTTTGATTACTCCA-TAGTAAAAGTTTAATAACCTTCC--
1 TGAAATTTTGATAAC-CCACTA-TGAAATTTTGATAACC-TCCTA
* * * * *
14410 T--AA-TTTGGTAACCATACAATGAAA-TTTGATAACTTCCCCA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCT-CCTA
* * * * *
14450 -G-AA-----AT-A-CCACTATGAAATTTTGGTAATCACATTT
1 TGAAATTTTGATAACCCACTATGAAATTTTGATAACCTC-CTA
* **
14484 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAA-CTCTCTA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCTC-CTA
* * * * *** *
14527 TAAAATTTTGTTGACCCCTCTATGAAATTTTGATATTTTCATTA
1 TGAAATTTTGAT-AACCCACTATGAAATTTTGATAACCTC-CTA
* * * **
14571 TGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCTC-CTA
* *
14615 TGAAATTTTGATAATCTTC-CTAT-TAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-C-CCACTATGAAATTTTGATAA-CC--TC-CTA
* * * *
14661 TGAAATTTCGATAA-TCACTTTATGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCCAC--TATGAAATTTTGATAACCTCCTA
* * * *
14703 TCAAATTTTGGT-ACTCC-TTATGAAATTAAGACTTTTATAACCTTCAC-A
1 TGAAATTTTGATAAC-CCACTATGAAA-T-----TTTGATAACC-TC-CTA
* ** * *
14751 TGAAATTTTGATAACCATACTAAAAAATTTTAATAACCACACTA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCTC-CTA
*
14795 TGAAATTTTGATAACCTTC-CTATGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGATAACC--CACTATGAAATTTTGA-TAACCTCC-TA
*
14839 TGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGCTA
1 TGAAATTTTGATAACC-CACTATGAAATT-TTGATAACCTC-CTA
* * *
14883 TGACATTTTG---A--CA--AT---CTCTTTGATAACCTTTCTA
1 TGAAATTTTGATAACCCACTATGAAAT-TTTGATAACC-TCCTA
* * **
14917 TAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACC-TCCTA
** * ** * *
14961 AAAAATTTTAATAACATGATCCTATGAAATTTTGGTAACCATACTA
1 TGAAATTTTGATAAC-CCA--CTATGAAATTTTGATAACC-TCCTA
* * *
15007 TGAAATTTTGATAACCTTC-CCAAGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACC--CACTATGAAATTTTGATAACCTCC-TA
* *
15051 TGAAATTTTGGTACCCACACTATGAAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACC-CACTATGAAATTTTGATAACCTCCT-A
* *
15095 TGAAATTATAATAA-CCATCTTATGAAATTTTGATAACC
1 TGAAATTTTGATAACCCA-C-TATGAAATTTTGATAACC
15133 ACACAGAGAC
Statistics
Matches: 728, Mismatches: 156, Indels: 188
0.68 0.15 0.18
Matches are distributed among these distances:
33 12 0.02
34 25 0.03
35 3 0.00
36 5 0.01
37 2 0.00
38 38 0.05
39 16 0.02
40 14 0.02
41 10 0.01
42 45 0.06
43 74 0.10
44 341 0.47
45 50 0.07
46 61 0.08
47 10 0.01
48 13 0.02
49 4 0.01
50 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (42 bp):
TGAAATTTTGATAACCCACTATGAAATTTTGATAACCTCCTA
Found at i:14509 original size:22 final size:22
Alignment explanation
Indices: 14460--14903 Score: 146
Period size: 22 Copynumber: 20.0 Consensus size: 22
14450 GAAATACCAC
* * *
14460 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
14483 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
*
14504 TATGAAATTTTGATAA-CTCTC
1 TATGAAATTTTGATAACCTCTT
* * * * *
14525 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
*** *
14547 TATGAAATTTTGATATTTTCAT
1 TATGAAATTTTGATAACCTCTT
* *
14569 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
** **
14592 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTT
14613 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCTCTT
* *
14633 CCTAT-TAATTTTGATAATCCGATCTC
1 --TATGAAATTTTGATAA-CC--TCTT
* * *
14659 TATGAAATTTCGATAATCACTT
1 TATGAAATTTTGATAACCTCTT
* *
14681 TATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCTT
* * *
14701 TATCAAATTTTGGT-A-CTCCT
1 TATGAAATTTTGATAACCTCTT
* *
14721 TATGAAATTAAGACTTTTATAACCT-TCA
1 TATGAAA-T-----TTTGATAACCTCT-T
*
14749 CATGAAATTTTGATAACCATAC--
1 TATGAAATTTTGATAACC-T-CTT
** * * **
14771 TAAAAAATTTTAATAACCACAC
1 TATGAAATTTTGATAACCTCTT
*
14793 TATGAAATTTTGATAACCT-TCC
1 TATGAAATTTTGATAACCTCT-T
* *
14815 TATGAAATATT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCTT
* * **
14837 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCTT
**
14859 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCTT
* * *
14881 TATGACATTTTGACAATCTCTT
1 TATGAAATTTTGATAACCTCTT
14903 T
1 T
14904 GATAACCTTT
Statistics
Matches: 305, Mismatches: 82, Indels: 69
0.67 0.18 0.15
Matches are distributed among these distances:
19 2 0.01
20 15 0.05
21 49 0.16
22 202 0.66
23 6 0.02
24 4 0.01
25 10 0.03
26 7 0.02
27 2 0.01
28 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:14820 original size:66 final size:65
Alignment explanation
Indices: 14735--15132 Score: 249
Period size: 66 Copynumber: 6.2 Consensus size: 65
14725 AAATTAAGAC
* *
14735 TTTT-ATAACCTTCAC-ATGAAATTTTGATAACCATACTAAAAAATTTTAATAACCACACTATGA
1 TTTTGATAACC-TCACTATGAAATTTTGATAACC-TCCTAAGAAATTTTAATAACCACACTATGA
14798 AA
64 AA
* * **
14800 TTTTGATAACCTTC-CTATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATG
1 TTTTGATAACC-TCACTATGAAATTTTGA-TAACCTCC-TAAGAAATTTTAATAACCACACTATG
14863 AAA
63 AAA
* * * * * *** *
14866 TTCTT-ATAACCTCGCTATGACATTTTGACAA--T-CT------CTTTGATAACCTTTCTATAAA
1 TT-TTGATAACCTCACTATGAAATTTTGATAACCTCCTAAGAAATTTTAATAACCACACTATGAA
14921 A
65 A
* * ** * *
14922 TTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAAAAATTTTAATAA-CATGATCCTAT
1 TTTTGATAACCTCACTATGAAATTTTGATAACC-TCCTAAGAAATTTTAATAACCA-CA--CTAT
14986 GAAA
62 GAAA
* * *
14990 TTTTGGTAACCAT-ACTATGAAATTTTGATAACCTTCCCAAGAAATTTTGATAACTTC-CA-TAT
1 TTTTGATAACC-TCACTATGAAATTTTGATAACC-TCCTAAGAAATTTTAATAAC--CACACTAT
15052 GAAA
62 GAAA
* * * * * *
15056 TTTTGGTACCCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATC-TTATGA
1 TTTTGATAACCTCACTATGAAATTTTGATAACCTCCT-AAGAAATTTTAATAACCA-CACTATGA
15120 AA
64 AA
15122 TTTTGATAACC
1 TTTTGATAACC
15133 ACACAGAGAC
Statistics
Matches: 258, Mismatches: 45, Indels: 59
0.71 0.12 0.16
Matches are distributed among these distances:
55 1 0.00
56 38 0.15
59 1 0.00
60 2 0.01
62 1 0.00
63 1 0.00
64 2 0.01
65 14 0.05
66 142 0.55
67 3 0.01
68 51 0.20
69 1 0.00
71 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (65 bp):
TTTTGATAACCTCACTATGAAATTTTGATAACCTCCTAAGAAATTTTAATAACCACACTATGAAA
Found at i:15010 original size:22 final size:22
Alignment explanation
Indices: 14901--15133 Score: 186
Period size: 22 Copynumber: 10.5 Consensus size: 22
14891 TGACAATCTC
* * *
14901 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATCCTATGAAAT
*
14923 TGTGATAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** * **
14945 TTCAATAACCTTCCTAAAAAAT
1 TTTGATAACCATCCTATGAAAT
* *
14967 TTTAATAACATGATCCTATGAAAT
1 TTTGATAAC--CATCCTATGAAAT
* *
14991 TTTGGTAACCATACTATGAAAT
1 TTTGATAACCATCCTATGAAAT
* * *
15013 TTTGATAACCTTCCCAAGAAAT
1 TTTGATAACCATCCTATGAAAT
*
15035 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
15057 TTTGGTACCCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
15079 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
15101 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
15123 TTTGATAACCA
1 TTTGATAACCA
15134 CACAGAGACA
Statistics
Matches: 165, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
21 7 0.04
22 136 0.82
23 6 0.04
24 16 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:15337 original size:20 final size:20
Alignment explanation
Indices: 15299--15337 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15289 TATTGGCATT
15299 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
15319 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
15338 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:17881 original size:20 final size:20
Alignment explanation
Indices: 17818--17886 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
17808 CAAAAAATTG
*
17818 TAGGGAGATTAACAAAATCTCA
1 TAGGAAGATT-ACAAAAT-TCA
* * *
17840 CAGAAAGATTATCAAAAATCA
1 TAGGAAGATTA-CAAAATTCA
*
17861 TAGGAAGGTTACAAAATTCA
1 TAGGAAGATTACAAAATTCA
17881 TAGGAA
1 TAGGAA
17887 AGTTTATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 14 0.37
21 12 0.32
22 12 0.32
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (20 bp):
TAGGAAGATTACAAAATTCA
Found at i:17960 original size:43 final size:44
Alignment explanation
Indices: 17912--18014 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
17902 CATAGTTAGG
* * * *
17912 TTATCAAAGTTTCATATGG-AGTTCATCACATTTTTATA-GATAA
1 TTATCAAAATTTCATATGGTAGTT-ATCAAAATTTAATAGGATAA
* * *
17955 TTATCAAAATTTTATATGGTGGTTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTCATATGGTAGTTATCAAAATTTAATAGGATAA
17999 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
18015 AAAATATACA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 28 0.56
44 22 0.44
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGTAGTTATCAAAATTTAATAGGATAA
Found at i:17966 original size:22 final size:22
Alignment explanation
Indices: 17943--18010 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
17933 TTCATCACAT
*
17943 TTTTATA-GATAATTATCAAAA
1 TTTTATAGGGTAATTATCAAAA
* **
17964 TTTTATATGGTGGTTATCAAAA
1 TTTTATAGGGTAATTATCAAAA
*
17986 TTTAATAGGGTAATTATCAAAA
1 TTTTATAGGGTAATTATCAAAA
18008 TTT
1 TTT
18011 CATAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 7 0.18
22 32 0.82
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (22 bp):
TTTTATAGGGTAATTATCAAAA
Done.